Polymer denitrification has received much attention in the field of advanced wastewater treatment. It can release carbon source stably during long-term operation, which can be used as electron donor for denitrification. However, the response of the polymer denitrification system to the transient changes of nitrate is not sufficiently disclosed yet. In this study, the response of a polymer denitrification system to nitrate was comprehensively investigated through a series of experiments. Therefore, real-time response and hysteresis response phenomena were identified. The time dependence of microorganisms in the system and the recovery of the hysteresis response were elucidated. The experimental results revealed distinct response patterns before and after the hysteresis tipping point. The denitrifying microorganisms, which showed a high adaptive capacity, exhibited a real-time response over a range of low nitrate concentration variations (∼20–30 mg/L). In contrast, microbial recovery is poor over a range of high nitrate concentration variation (∼35–40 mg/L), which is referred to as a hysteresis response. Finally, the hysteresis response mechanism was revealed by monitoring the recovery of denitrification enzymes, gene and microbial communities. The results showed that transient shocks of high nitrate loads affect microbial community structure stability, denitrifying enzyme activity and gene expression. Meanwhile, the abundance of Microbacterium associated with carbon release was reduced. The combination of these factors leads to a hysteresis response in denitrification and carbon release. This work contributes to a deeper understanding of the hysteresis behavior in polymer denitrification systems, offering critical insights for optimizing system performance and improving nitrogen removal efficiency.